Now, our exclusive conversation with retired marine corps general john allen who served most recently as commander in afghanistan. His retirement last month after turning down a nato command was understandable given the toll on his family and being drawn into the controversy over cia director david petraeus who resigned after revealing an affair. General allen was cleared in that investigation and we spoke with him and his wife kathy at their home in virginia. You were in the middle of prosecuting a war with so many young people's lives at your hands and the investigation happens. Well, I was notified that e-mails were -- had become known, that was going to require an investigation into the appropriateness of a relationship. And I had to reflect on whether I could remain in command. I believe I could. In fact, I felt an obligation to a duty to remain in command. I had to deal with the realities of something that was going on back here. I won't tell you that there wasn't a lot of pressure in that regard. But my sense of duty to the war effort and my sense of duty the troops. That remain focus on that. Reporter: The thousands of e-mails spanning a three-year period were between john allen and florida socialite jill kellie. He was assigned to central command in tampa. Investigators launched an inquiry to see if there was anything inappropriate in the e-mails. A senior defense official immediately said there were 20, 30,000 e-mails. Mrs. Allen, what did you think when you first heard that? The funny the thing is, because I got so many e-mails everfrom the same person -- jill kelley? Yes, always very friendly. Always -- I always used terms of endearment. He always used terms of endearment. Sweetie, dear? Absolutely. When someone shares an e-mail with her husband, you know, i thought is someone thinking this is a little odd that they're taking this so seriously? I mean, I have a lot of faith in him. I have a lot of faith in our relationship. My biggest concern was for him. Because I thought, I don't know how he can run a war and then have this added pressure. Did you ever think on dear? What did I say in those e-mails? Any time you're investigated and you have to remember back across three years, I didn't have any concern about what the content of the e-mails, I was just interested in putting behind me as quickly as we could. You were worried for a time about his health? Absolutely. My concerns caused me to have -- you know, I had some issues before because I have autoimmune issues. But when this broke, it really took a toll on me. Reporter: Further adding to your stress? Every phone call was pretty grim. And they were getting worse by the minute. For many years I had told kathy as we had dealt with these issues that the day that this becomes too big I will drop my letter the next day. She wasn't going to tell me when I was afraid where this was going to end up. Reporter: In late april a retirement ceremony was held for general allen. An emotional affair. Among the guests david and holly petraeus. David and holly petraeus are like family. Given all that we had to experience together. I couldn't retire without asking david and holly petraeus to be present. Reporter: I assume you haven't really talked about what happened? That's right. It doesn't require that we have a conversation about it. Reporter: What allen does want to talk about, does want people to remember is the troops, during husband retirement he spoke movingly about those who he lost during his command in afghanistan. 561 troops you lost. That's a number that you'll never forget? That's right. I think about it all the time. There's a moment of reflection about those 561 empty chairs around dinner tables, when families gather for christmas from now on or they gather for easter and some precious member of the family, they're gone forever. And that's a generational loss. Because the family will be different. The children will be different. Every one of those losses has to mean something. Reporter: There are some very moving images of you at those memorial services. What was the hardest one? This particular ceremony was for three sets of remains. And the wife of one of the soldiers was in an adjacent unit. I'll remember her gripping the coffin, crying his name. In the back of the c-130. I'll never forget that.Cause there was the catastrophe of the loss playing out in front of our eyes. As we sending that young soldier home forever. Reporter: The largest loss of life came in a single incident in august 2011, 30 americans, MOSTLY NAVY S.E.A.L.s WERE Killed when their helicopter was shot down. 4:00 in the morning. Initial call was that we got a bird down. Doesn't look good. Then the next call came in and said that it was a catastrophic crash and we probably lost everyone. The loss was great. And it was a grim night. It was a grim night. After the ceremony was over, he wenfound the people who prepared those caskets, and one by one, he thanked them for what they had done. He said I know this must have been hard on you. There was a healing that took place. Reporter: When you look at what's happening there now in afghanistan, we have been taking more casualties of late, what does that tell you about what's happening now? I think the taliban are fighting for their lives right now. We have seen success by the afghan national security forces. The taliban has recognized that we're not going anywhere. Eventually our numbers will come down, pretty significantly, but there's going to be an international military presence in afghanistan for a long time. Reporter: And you believe that it's absolutely necessary that we remain? No question. Our forces will continue to train the afghan forces well after 2014. Reporter: But iraq is a different story. Yot a good deal of time in some of the toughest periods in iraq and you see it today, are you alarmed at all by what's happening there? I am. My fear is that we could see the polarization of the elements in iraq. Increase in violence. Those who served there, especially those who served in the province which was a dangerous area, we don't want it to return there. The iraqi leadership was unable to put together the political will necessary to give us the guarantees that we needed to ultimately station a large force there. Reporter: Things would better off today in iraq? We also asked general allen about the alarming almost daily revelations of military sexual assault. This is a leadership issue. Commanders can't be ambiguous about this. We can't not talk about that. Commanders have to stand in front of their units and tell people about they expect. Because silence isn't good enough. Reporter: Allen said that leading the many soldiers, sailors, airmen and marines has been his proudest accomplishment. The young men and women through generations who we should all be thinking of this memorial day. This is an opportunity for all americans to think not just about the troops in uniform today but what everyone has done, the sacrifices of all of our troops for so long to give this country the quality of life that it has and the freedom that we enjoy every single day. Our thanks to kathy and general allen who's taking on a new role, advising defense secretary chuck hagel on middle east peace talks.

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